An Overview of Phytophthora Root and Stem Rot

Introduction

Phytophthora root and stem rot, caused by two Phytophthora species, is a soilborne disease known for its devastating impact on soybean. It is a globally important disease and has caused significant losses in the United States and Canada. Planting susceptible varieties in poorly drained fields with a history of the disease can lead to season-long problems. These include reduced plant stands and the need to replant early in the season, plant death and stunting throughout the season, and yield losses of up to 100% (Figure 1). This publication provides an overview of the latest information on the identification, biology, and management of Phytophthora root and stem rot in soybean.

Symptoms

Symptoms of Phytophthora root and stem rot can be observed shortly after planting. Seed may rot in the ground and/or seedlings may not emerge (pre-emergence damping-off). Seedlings can also exhibit post-emergence damping-off symptoms such as stunting and brown, rotted roots, wilting leaves, yellow leaves (chlorosis), water-soaked lesions on stems, and plant death (Figure 2).

Later in the season, the signature symptom of  Phytophthora root and stem rot is a chocolate-brown/purple lesion on the stem (Figure 3). This lesion typically begins below the soil line and can extend up past multiple nodes on the stem. Lesions can encircle the stem or may only be present on one side of the stem. Other symptoms include root rot, yellowing between leaf veins (interveinal chlorosis), wilting, stunting, and premature plant death. In varieties with partial resistance, discolored roots, and stunting may be observed; but plants typically survive the infection.

Disease Cycle

The primary pathogen that causes Phytophthora root and stem rot is Phytophthora sojae, although P. sansomeana has also been associated with Phytophthora root and stem rot in several states. Phytophthora is not a true fungus, but a fungus-like organism classified as an oomycete and commonly referred to as a water mold. There are multiple pathotypes (formerly known as races) of P. sojae that can influence the management of Phytophthora root and stem rot. The pathotypes present in a field can be influenced by geography and the type of soybean resistance to Phytophthora root and stem rot that is present in the planted soybean.

Phytophthora survives on crop residue or in the soil as long-lived resting structures called oospores (Figure 4). Warm (at least 70°F or 21°C), saturated soil induces oospores to germinate and produce swimming spores called zoospores. These zoospores are attracted to soybean roots by chemicals produced by the root system. The zoospores infect roots, and then the pathogen colonizes the plant. Soybean plants can be infected at any growth stage. Oospores can survive for many years in soil and do not all germinate at the same time.

Conditions that Favor Disease

Fields with areas of poorly drained soil, soils high in clay content or organic matter, soil compaction, and low spots where excess water pools provide conducive environments for disease development. Warm (at least 70°F or 21°C) soil temperatures favor disease development, and periods of heavy rain anytime during the season can provide environmental conditions suitable for disease. Compacted soils prevent plants from forming healthy root systems and do not drain well, increasing disease risk. Reduced tillage systems may increase the risk of damping-off caused by P. sojae. This is because greater populations of the pathogen are present near the soil surface compared to conventionally tilled fields where the greatest pathogen numbers are found six inches below the soil surface. Continuous soybean planting and short rotations allow soilborne inoculum levels to build up, which can increase the risk of Phytophthora root and stem rot.

Yield Losses and Impact

From 1996 to 2023, the estimated average annual soybean loss from Phytophthora root and stem rot in the United States and Canada was over 35 million bushels. Phytophthora root and stem rot has the potential to result in soybean yield losses of up to 100%, but this number varies depending on disease severity and timing of disease onset.

Diagnosis

Phytophthora root and stem rot is often first observed as reduced plant populations, or gaps in plant stand where seedlings have not emerged or died. Reduced stand occurs with many soybean seedling diseases, and laboratory diagnosis may be required to verify that reductions in plant populations are associated with Phytophthora root and stem rot. During the middle of the season, disease may be observed on single plants, small groups of plants, or large patches across the field. The classic stem lesion may be visible on plants. One notable late-season diagnostic feature of Phytophthora root and stem rot is that the leaves remain on plants that die prematurely in the field (Figure 5). Besides root rots, diseases such as stem canker, white mold, red crown rot, and pest damage, such as that caused by soybean gall midge, can be confused with Phytophthora root and stem rot from the field edge. Therefore it is important to examine the affected areas, especially late in the season.

Root rot pathogens can be difficult to diagnose correctly without the assistance of trained laboratory personnel. Submission of unknown samples to diagnostic clinics is recommended for accurate identification. 

Diseases, Disorders, and Injury with Similar Symptoms

Flooding

Flooding suffocates soybean roots and nodules, leading to plant stress. Affected plants may turn yellow, wilt prematurely due to oxygen deprivation and CO₂ buildup, and eventually disintegrate. Flooded areas typically accumulate crop residue and may emit odors due to anaerobic conditions (Figure 6). Symptoms of flooding injury may be observed on roots and the outer cortical tissue, which may detach easily exposing white root steles. Flood-affected plants may develop adventitious roots.

Furthermore, nodules may die and lose their pink coloration, indicating deteriorating health. Plants can recover from flooding injury, especially during periods followed by cloudy and cool weather conditions. However, the extent of recovery in specific areas depends on weather conditions and the duration of saturation in the field.

How to distinguish flooding from Phytophthora root and stem rot: Nodules on plants affected solely by Phytophthora root and stem rot (but still alive) will maintain their normal color and should be pink when cut in half. If plants have died prematurely due to PRR, a laboratory diagnosis may be needed to confirm symptoms.

Other seedling diseases

Several species of Pythium can cause both pre- and post-emergence seedling blight and damping-off. The infected seed exhibits symptoms of rotting and water-soaking. Furthermore,  infected seedlings display water-soaked lesions on the hypocotyls and/or cotyledons, which later progress into a brown soft rot (Figure 7). Rhizoctonia infection affects seedlings, which leads to pre- and post-emergence seedling rot as well as damping-off. Reddish-brown lesions that appear sunken, firm, dry, and are primarily confined to the outer layer of tissue may be observed on the hypocotyl of infected plants (Figure 8). Symptoms can be particularly severe in fields with light and sandy soils. Fusarium infections also lead to seedling rot and damping off before and after germination. Infected seedlings have discolored roots ranging from reddish-brown to dark brown. Mature plants may have smaller root systems characterized by purplish-brown discoloration and inadequate nodulation that ultimately cause wilting and premature death.

How to distinguish other seedling diseases (Pythium, Rhizoctonia, Fusarium) from Phytophthora root and stem rot: It is difficult to distinguish seedling diseases caused by P. sojae from other seedling disease pathogens. Sending samples for laboratory diagnosis is the most accurate way to confirm which seedling disease is affecting plants.

Other stem diseases (stem canker, red crown rot, and white mold)

During the season, it is crucial to thoroughly inspect affected areas, as other stem diseases can be mistaken for Phytophthora root rot, especially from the field edge. Other stem diseases are also capable of prematurely killing soybean plants.

Stem Canker

Brown lesions, sometimes sunken, starting from aboveground nodes are characteristic of stem canker (Figure 9). Consequently, the stem of a soybean plant with stem canker typically remains green and healthy at the soil line, and the roots remain healthy.

How to distinguish stem canker from Phytophthora root and stem rot: Stem canker lesions typically do not extend all the way to the soil line, while Phytophthora root and stem rot lesions start from below the soil line and extend up the stem for several nodes. Root rot symptoms may also be present with Phytophthora root and stem rot.

Red Crown Rot

Red crown rot (RCR) symptoms on plant stems are characterized by reddish, sunken lesions located just above the soil line that might extend a few inches up the stem. As the disease progresses, reddish-orange fungal structures (called perithecia) will become visible on the stem's surface near the soil line (Figure 10). The foliar symptoms of RCR can be similar to those caused by sudden death syndrome (SDS) or brown stem rot (BSR). 

How to distinguish red crown rot from Phytophthora root and stem rot: Plants affected by Phytophthora root and stem rot will not have reddish-orange fungal structures visible on the stem.

White Mold

Symptoms of white mold can include water-soaked stem lesions that rapidly progress above and below infected nodes and eventually encircle the stem. Over time, infected stems become bleached and stringy. Lesions can also occur on pods, petioles, and, rarely, on leaves. White, fluffy cotton-like growth may be observed on the bleached stems. Severe infection weakens the plant and can result in wilting, lodging, and death. White mold often occurs in patches in the field.

How to distinguish white mold from Phytophthora root and stem rot: White mold produces white cottony, mycelia (moldy growth), bleached stems, and sclerotia on infected plant tissues (Figure 11). Sclerotia may be produced inside or outside of stems and pods. Phytophthora does not produce cottony growth or sclerotia.

Soybean gall midge

Soybean gall midge symptoms result in galling at the base of the stem, which can resemble lesions characteristic of Phytophthora root and stem rot. Prematurely dead plants may retain their leaves. 

How to distinguish soybean gall midge from Phytophthora root and stem rot: Look for dark, discolored areas near the base of the stem and peel the blackened tissue back to look for small (up to 1/12 inch or 2 mm long) white or orange larvae (Figure 12). Plants affected by Phytophthora root and stem rot typically do not form galls.

Management

Cultural Practices

Cultural management practices may have a limited impact on this disease. Oospores survive in the soil for many years, and crop rotation is unlikely to substantially reduce the disease risk. Additionally, P. sansomeana can infect corn, so in areas where that pathogen is present, traditional crop rotation patterns will be less effective at managing disease. Improving field drainage, such as the use of drain tile, may help to reduce favorable soil conditions for disease development. Tillage may improve soil conditions but will not lead to a reduction of pathogen populations. Tillage may also spread Phytophthora oospores across a field, increasing their distribution and potential impact.

Fungicide Seed Treatments

Seed treatments can play an important role in Phytophthora root and stem rot management. There are several active ingredients available with efficacy against oomycetes like Phytophthora including mefenoxam (Apron XL LS), metalaxyl (AllegianceFL/AllegianceLS), oxathiapiprolin (Lumisena), ethaboxam (Intego), and picarbutrazox (Vayantis, Cruiser Maxx APX, Warden CX 2.0). Fields with a history of Phytophthora root and stem rot should be planted with seeds with a seed treatment package including one of the above active ingredients and at effective rates to control oomycete pathogens. This may necessitate increasing the rate (seed load) of the active ingredient used in the seed treatment (Table 1) in fields prone to Phytophthora root and stem rot.

Metalaxyl and mefenoxam have been in use for decades as seed treatment or in-furrow application for oomycete pathogens. Recent fungicide sensitivity testing of P. sojae within the United States to common seed treatment compounds such as mefenoxam, ethaboxam, and oxathiapiprolin identified no insensitivity or resistance to the compounds within the sampled population. Seed treatments, unlike foliar sprays or in-furrow applications, are applied to the seed only once a year and manage the microbial community directly around the seed itself. This confines the selection for resistant genotypes to a smaller physical area and minimizes selection pressure throughout the entire season, thereby reducing the risk of fungicide resistance developing in the population.

Table 1. List of active ingredients for the control of oomycete pathogens such as Phytophthora as of March 2024. Efficacy ratings for active ingredients are available in Fungicide Efficacy for Control of Soybean Seedling Diseases

¹This is not a complete list of products (trade names) available for each active ingredient. Other fungicide products with these active ingredients may be available for use against Phytophthora spp.

Foliar Fungicides

There are no foliar fungicides with efficacy against Phytophthora root and stem rot.

Resistant Varieties

Soybean varieties with resistance to Phytophthora root and stem rot are commercially available. Two types of resistance exist: (i) complete resistance and (ii) partial resistance, commonly referred to as field tolerance. Complete resistance is mediated by single Rps (resistance to P. sojae) genes that recognizes corresponding genes in P. sojae, and consequently activates the plant’s defense system. There are five Rps genes available (Rps1a, Rps1c, Rps1k, Rps3a, and Rps6) in commercial varieties, but over 30 Rps genes have been identified. The commercially available Rps genes are not effective against P. sansomeana.

Partial resistance is controlled by multiple genes and is only triggered after the first true leaves emerge. Thus, a seed treatment may provide protection against infection until partial resistance is activated. While partial resistance does not completely suppress P. sojae infection, the disease is less severe, and plants can survive infection and produce grain, although yield may be reduced. Partial resistance limits P. sojae root infection and colonization. Varieties with partial resistance may reduce the number of new oospores, or pathogen inoculum, produced for the next season. Commercial varieties have varying levels of partial resistance. Farmers are advised to select varieties that include effective Rps genes for their area, if known, and a high level of partial resistance (Figure 13). Check with your seed supplier or local extension specialist for varieties with the appropriate Rps genes for your area.

Pathotypes

In the past, individual P. sojae strains (isolates) were characterized into races based on their ability to cause infection on plants with specific Rps genes. Now that over 30 Rps genes have been identified, and the term race has become obsolete. Instead, the term “pathotype” is used to describe P. sojae strains that cause disease on cultivars that contain specific Rps genes. For example P. sojae strains that cause disease on cultivars containing Rps1a and Rps1k would have a pathotype of 1a,1k. 

Rps genes have been used since the 1960s, and the repeated use of these genes has caused shifts in the populations of P. sojae, so that Phytophthora root and stem rot may not be managed by soybean varieties containing certain Rps genes. Recent surveys of P. sojae populations in the Midwest and Canada reported soybean varieties with Rps1a, Rps1c, and Rps1k are unlikely to control Phytophthora root and stem rot in many areas. In contrast, varieties with Rps3a and Rps6 still provide effective control.

Management of Phytophthora root and stem rot is complicated and requires an integrated approach. Using a combination of cultural practices, seed treatments, and varieties with effective Rps genes and partial resistance will be most effective at reducing disease impact.

Find Out More

Other publications in the Soybean Disease Management series are available on the Crop Protection Network website (cropprotectionnetwork.org).

References

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Acknowledgements

Authors

Horacio Lopez-Nicora, The Ohio State University; Dylan Mangel, University of Nebraska-Lincoln; Austin McCoy, Michigan State University; Richard W. Webster, North Dakota State University; Alison Robertson, Iowa State University; Martin Chilvers, Michigan State University; Albert Tenuta, Ontario Ministry of Food, Agriculture and Rural Affairs; Daren Mueller, Iowa State University; and Kiersten Wise, University of Kentucky.

Reviewers

Tom W. Allen, Mississippi State University; Nolan Anderson, Texas A&M University; Gary C. Bergstrom, Cornell University; Mandy D. Bish, University of Missouri; Maira R. Duffeck, Oklahoma State University; Travis R. Faske, University of Arkansas; Dean Malvick, University of Minnesota; Darcy Telenko, Purdue University; and Damon L. Smith, University of Wisconsin-Madison.

The authors thank The United Soybean Board and the Grain Farmers of Ontario for their support.